The rust isnt 'on the paint', its in the metal underneath and 'bubbling' up. through the voids in the paint. It can kind of overflow over the surrounding paint and look bigger; you see that on chromed parts that you steel wool the rust off of, a small pit can really look big until the rust scale is gone. Chrome is tough though, and the rust on the painted areas might not be as small as you would hope.
If you can soften the scale you can scrape it off. The key to using scrapers is to use something softer than the surface, in this case paint. An old credit card wont hurt the paint, and even aluminum wont be as harsh as steel. Try dabbing some light bodied oil (3 in 1, penetrating oil, etc,) on a rust spot with a Q-Tip and let soak. If it goes dryish, do it again. Let this get into and under the scale and take the scraper to it. Use a magnifier if you cant see that you are working on just the rusty spot. As you scrape down through the scale it will look dry again, so add some oil. You will get a feel and eye for this pretty quick, but it is futzy, so have some refreshment handy and get comfortable. With good magnification and some experience you can go to 'harsher' scrapers but always start with the softest to feel it out.